A standard protocol to report discrete stage-structured demographic information

Samuel J.L. Gascoigne; Simon Rolph; Daisy Sankey; Nagalakshmi Nidadavolu; Adrian S. Stell Pičman; Christina M. Hernández; Matthew E.R. Philpott; Aiyla Salam; Connor Bernard; Erola Fenollosa; Young Jun Lee; Jessica McLean; Shathuki Hetti Achchige Perera; Oliver G. Spacey; Maja Kajin; Anna C. Vinton; C. Ruth Archer; Jean H. Burns; Danielle L. Buss; Hal Caswell; Judy P. Che-Castaldo; Dylan Z. Childs; Pol Capdevila; Aldo Compagnoni; Elizabeth Crone; Thomas H.G. Ezard; Dave Hodgson; Tiffany M. Knight; Owen R. Jones; Eelke Jongejans; Jenni McDonald; Brigitte Tenhumberg; Chelsea C. Thomas; Andrew J. Tyre; Satu Ramula; Iain Stott; Raymond L. Tremblay; Phil Wilson; James W. Vaupel; Roberto Salguero-Gómez

doi:10.1111/2041-210X.14164

A standard protocol to report discrete stage-structured demographic information

Samuel J.L. Gascoigne^* (Co-auteur), Simon Rolph, Daisy Sankey, Nagalakshmi Nidadavolu, Adrian S. Stell Pičman, Christina M. Hernández, Matthew E.R. Philpott, Aiyla Salam, Connor Bernard, Erola Fenollosa, Young Jun Lee, Jessica McLean, Shathuki Hetti Achchige Perera, Oliver G. Spacey, Maja Kajin, Anna C. Vinton, C. Ruth Archer, Jean H. Burns, Danielle L. Buss, Hal CaswellJudy P. Che-Castaldo, Dylan Z. Childs, Pol Capdevila, Aldo Compagnoni, Elizabeth Crone, Thomas H.G. Ezard, Dave Hodgson, Tiffany M. Knight, Owen R. Jones, Eelke Jongejans, Jenni McDonald, Brigitte Tenhumberg, Chelsea C. Thomas, Andrew J. Tyre, Satu Ramula, Iain Stott, Raymond L. Tremblay, Phil Wilson, James W. Vaupel, Roberto Salguero-Gómez^* (Co-auteur)

^*Bijbehorende auteur voor dit werk

NIOO - Animal Ecology (AnE)

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

2 Citaten (Scopus)

Samenvatting

Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.

Originele taal-2	Engels
Tijdschrift	Methods in Ecology and Evolution
DOI's	https://doi.org/10.1111/2041-210X.14164
Status	E-pub ahead of print - 20 jun. 2023

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10.1111/2041-210X.14164Licentie: CC BY

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Gascoigne, S. J. L., Rolph, S., Sankey, D., Nidadavolu, N., Stell Pičman, A. S., Hernández, C. M., Philpott, M. E. R., Salam, A., Bernard, C., Fenollosa, E., Lee, Y. J., McLean, J., Hetti Achchige Perera, S., Spacey, O. G., Kajin, M., Vinton, A. C., Archer, C. R., Burns, J. H., Buss, D. L., ... Salguero-Gómez, R. (2023). A standard protocol to report discrete stage-structured demographic information. Methods in Ecology and Evolution. Online publicatie vooraf. https://doi.org/10.1111/2041-210X.14164

@article{7439b8478fae4dae85b06b9379938447,

title = "A standard protocol to report discrete stage-structured demographic information",

abstract = "Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.",

keywords = "comparative demography, matrix population models, open access, reproducibility",

author = "Gascoigne, {Samuel J.L.} and Simon Rolph and Daisy Sankey and Nagalakshmi Nidadavolu and Stell Pi{\v c}man, {Adrian S.} and Hern{\'a}ndez, {Christina M.} and Philpott, {Matthew E.R.} and Aiyla Salam and Connor Bernard and Erola Fenollosa and Lee, {Young Jun} and Jessica McLean and Shathuki Hetti Achchige Perera and Spacey, {Oliver G.} and Maja Kajin and Vinton, {Anna C.} and Archer, {C. Ruth} and Burns, {Jean H.} and Buss, {Danielle L.} and Hal Caswell and Che-Castaldo, {Judy P.} and Childs, {Dylan Z.} and Pol Capdevila and Aldo Compagnoni and Elizabeth Crone and Ezard, {Thomas H.G.} and Dave Hodgson and Knight, {Tiffany M.} and Jones, {Owen R.} and Eelke Jongejans and Jenni McDonald and Brigitte Tenhumberg and Thomas, {Chelsea C.} and Tyre, {Andrew J.} and Satu Ramula and Iain Stott and Tremblay, {Raymond L.} and Phil Wilson and Vaupel, {James W.} and Roberto Salguero-G{\'o}mez",

note = "Data archiving: no NIOO data",

year = "2023",

month = jun,

day = "20",

doi = "10.1111/2041-210X.14164",

language = "English",

journal = "Methods in Ecology and Evolution",

issn = "2041-210X",

publisher = "John Wiley and Sons Ltd",

}

Gascoigne, SJL, Rolph, S, Sankey, D, Nidadavolu, N, Stell Pičman, AS, Hernández, CM, Philpott, MER, Salam, A, Bernard, C, Fenollosa, E, Lee, YJ, McLean, J, Hetti Achchige Perera, S, Spacey, OG, Kajin, M, Vinton, AC, Archer, CR, Burns, JH, Buss, DL, Caswell, H, Che-Castaldo, JP, Childs, DZ, Capdevila, P, Compagnoni, A, Crone, E, Ezard, THG, Hodgson, D, Knight, TM, Jones, OR, Jongejans, E, McDonald, J, Tenhumberg, B, Thomas, CC, Tyre, AJ, Ramula, S, Stott, I, Tremblay, RL, Wilson, P, Vaupel, JW & Salguero-Gómez, R 2023, 'A standard protocol to report discrete stage-structured demographic information', Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.14164

TY - JOUR

T1 - A standard protocol to report discrete stage-structured demographic information

AU - Gascoigne, Samuel J.L.

AU - Rolph, Simon

AU - Sankey, Daisy

AU - Nidadavolu, Nagalakshmi

AU - Stell Pičman, Adrian S.

AU - Hernández, Christina M.

AU - Philpott, Matthew E.R.

AU - Salam, Aiyla

AU - Bernard, Connor

AU - Fenollosa, Erola

AU - Lee, Young Jun

AU - McLean, Jessica

AU - Hetti Achchige Perera, Shathuki

AU - Spacey, Oliver G.

AU - Kajin, Maja

AU - Vinton, Anna C.

AU - Archer, C. Ruth

AU - Burns, Jean H.

AU - Buss, Danielle L.

AU - Caswell, Hal

AU - Che-Castaldo, Judy P.

AU - Childs, Dylan Z.

AU - Capdevila, Pol

AU - Compagnoni, Aldo

AU - Crone, Elizabeth

AU - Ezard, Thomas H.G.

AU - Hodgson, Dave

AU - Knight, Tiffany M.

AU - Jones, Owen R.

AU - Jongejans, Eelke

AU - McDonald, Jenni

AU - Tenhumberg, Brigitte

AU - Thomas, Chelsea C.

AU - Tyre, Andrew J.

AU - Ramula, Satu

AU - Stott, Iain

AU - Tremblay, Raymond L.

AU - Wilson, Phil

AU - Vaupel, James W.

AU - Salguero-Gómez, Roberto

N1 - Data archiving: no NIOO data

PY - 2023/6/20

Y1 - 2023/6/20

N2 - Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.

AB - Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.

KW - comparative demography

KW - matrix population models

KW - open access

KW - reproducibility

U2 - 10.1111/2041-210X.14164

DO - 10.1111/2041-210X.14164

M3 - Article

AN - SCOPUS:85163042070

SN - 2041-210X

JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

ER -

A standard protocol to report discrete stage-structured demographic information

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